Effects of secondary electron emission (SEE) on the performance of a 6-cavity relativistic magnetron with transparent cathodes are probed through particle-in-cell simulations. Appropriate relations for the secondary electron yield have been developed and used. For comparisons, separate simulations have been performed with- and without electron cascading. Simulation results seem to indicate SEE to be detrimental to the power output due to deviations in the starting trajectories of secondary electrons, and the reduced fraction with synchronized rotational velocity. A higher reduction in output power is predicted with electron cascading, though mode competition was not seen at the 0.65 T field. A possible solution to mitigating SEE in magnetrons for high power microwave applications would be to alter the surface properties of emitting electrodes through irradiation, which can lead to graphitic film formation.